Shapeworks: Error in reflectMeshes when running femur and femur_cut use case

Created on 18 Feb 2021 · 12Comments · Source: SCIInstitute/ShapeWorks

Tried to run femur and femur_cut use case:

Tiny test works fine python RunUseCase.py --use_case femur --tiny_test
Use case runs well if you use --skip_grooming
Use case fails when you run python RunUseCase.py --use_case femur and python RunUseCase.py --use_case femur_cut with the error:

Step 2. Groom - Data Pre-processingInput filename: Output/femur/femur-v0/meshes/m09_R_femur.ply
Output filename: Output/femur/groomed/reflected/segmentations/m09_R_femur.reflect.ply
Traceback (most recent call last):
  File "RunUseCase.py", line 79, in <module>
    module.Run_Pipeline(args)
  File "/home/sci/iyerkrithika/ShapeWorks/Examples/Python/femur.py", line 219, in Run_Pipeline
    reflectedFiles_mesh = reflectMeshes(groomDir + 'reflected', files_mesh, reference_side)
  File "/home/sci/iyerkrithika/ShapeWorks/Examples/Python/GroomUtils.py", line 344, in reflectMeshes
    mesh.reflect(X, mesh.center()).write(seg_out)
ValueError: vector::reserve

QA bug

Source

iyerkrithika21

Most helpful comment

@iyerkrithika21 I think the crop function works fine. Increase the padding.

archanasri on 19 Feb 2021

👍2

All 12 comments

Running this on the latest from this branch, I get:

Input filename: Output/femur/groomed/centered/segmentations/m12_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m12_R_femur.reflect.isores.pad.com.center.aligned.nrrd
Input filename: Output/femur/groomed/centered/segmentations/m13_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m13_R_femur.reflect.isores.pad.com.center.aligned.nrrd
ERROR: In ../Common/DataModel/vtkIterativeClosestPointTransform.cxx, line 270
vtkIterativeClosestPointTransform (0x7ff2ceeb98c0): Can't execute with nullptr or empty input

Input filename: Output/femur/groomed/centered/segmentations/m14_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m14_R_femur.reflect.isores.pad.com.center.aligned.nrrd
Input filename: Output/femur/groomed/centered/segmentations/m15_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m15_R_femur.reflect.isores.pad.com.center.aligned.nrrd

Is this a problem?

akenmorris on 19 Feb 2021

I ran:

python RunUseCase.py --use_case femur

I answered 'yes' when it asks about rasterizing isotropic.

It ended with:


Input filename: Output/femur/groomed/clipped_segmentations/m03_L_femur.isores.pad.com.center.aligned.clipped.nrrd
Output filename: Output/femur/groomed/cropped/segmentations/m03_L_femur.isores.pad.com.center.aligned.clipped.cropped.nrrd
Traceback (most recent call last):
  File "RunUseCase.py", line 79, in <module>
    module.Run_Pipeline(args)
  File "/Users/amorris/sci/data/Examples/Python/femur.py", line 299, in Run_Pipeline
    croppedFiles_segmentations = applyCropping(groomDir + "cropped/segmentations", clippedFiles_segmentations, groomDir + "clipped_segmentations/*.nrrd")
  File "/Users/amorris/sci/data/Examples/Python/GroomUtils.py", line 225, in applyCropping
    img.crop(region).write(outname)
RuntimeError: /Users/amorris/sci/shapeworks/dependencies/build/ITK/Modules/Core/Common/src/itkDataObject.cxx:385:
Requested region is (at least partially) outside the largest possible region.

akenmorris on 19 Feb 2021

I ran:

python RunUseCase.py --use_case femur

I answered 'yes' when it asks about rasterizing isotropic.

It ended with:


Input filename: Output/femur/groomed/clipped_segmentations/m03_L_femur.isores.pad.com.center.aligned.clipped.nrrd
Output filename: Output/femur/groomed/cropped/segmentations/m03_L_femur.isores.pad.com.center.aligned.clipped.cropped.nrrd
Traceback (most recent call last):
  File "RunUseCase.py", line 79, in <module>
    module.Run_Pipeline(args)
  File "/Users/amorris/sci/data/Examples/Python/femur.py", line 299, in Run_Pipeline
    croppedFiles_segmentations = applyCropping(groomDir + "cropped/segmentations", clippedFiles_segmentations, groomDir + "clipped_segmentations/*.nrrd")
  File "/Users/amorris/sci/data/Examples/Python/GroomUtils.py", line 225, in applyCropping
    img.crop(region).write(outname)
RuntimeError: /Users/amorris/sci/shapeworks/dependencies/build/ITK/Modules/Core/Common/src/itkDataObject.cxx:385:
Requested region is (at least partially) outside the largest possible region.

Increasing the padding to 30 on line 259 in femur.py does not produce this error.
I will discuss this with @archanasri to find what is going wrong with the crop function.

iyerkrithika21 on 19 Feb 2021

@iyerkrithika21 I think the crop function works fine. Increase the padding.

archanasri on 19 Feb 2021

👍2

Running this on the latest from this branch, I get:

Input filename: Output/femur/groomed/centered/segmentations/m12_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m12_R_femur.reflect.isores.pad.com.center.aligned.nrrd
Input filename: Output/femur/groomed/centered/segmentations/m13_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m13_R_femur.reflect.isores.pad.com.center.aligned.nrrd
ERROR: In ../Common/DataModel/vtkIterativeClosestPointTransform.cxx, line 270
vtkIterativeClosestPointTransform (0x7ff2ceeb98c0): Can't execute with nullptr or empty input

Input filename: Output/femur/groomed/centered/segmentations/m14_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m14_R_femur.reflect.isores.pad.com.center.aligned.nrrd
Input filename: Output/femur/groomed/centered/segmentations/m15_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m15_R_femur.reflect.isores.pad.com.center.aligned.nrrd

Is this a problem?

@akenmorris what did you run from the command line?

archanasri on 19 Feb 2021

Running this on the latest from this branch, I get:

Input filename: Output/femur/groomed/centered/segmentations/m12_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m12_R_femur.reflect.isores.pad.com.center.aligned.nrrd
Input filename: Output/femur/groomed/centered/segmentations/m13_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m13_R_femur.reflect.isores.pad.com.center.aligned.nrrd
ERROR: In ../Common/DataModel/vtkIterativeClosestPointTransform.cxx, line 270
vtkIterativeClosestPointTransform (0x7ff2ceeb98c0): Can't execute with nullptr or empty input

Input filename: Output/femur/groomed/centered/segmentations/m14_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m14_R_femur.reflect.isores.pad.com.center.aligned.nrrd
Input filename: Output/femur/groomed/centered/segmentations/m15_R_femur.reflect.isores.pad.com.center.nrrd
Output filename: Output/femur/groomed/aligned/m15_R_femur.reflect.isores.pad.com.center.aligned.nrrd

Is this a problem?

@akenmorris what did you run from the command line?

@archanasri I get this when I run python RunUseCase.py --use_case femur --groom_images
I see this error in the rigid alignment step.

iyerkrithika21 on 19 Feb 2021

I believe I just ran:

python RunUseCase.py --use_case femur

akenmorris on 19 Feb 2021

The full use case without grooming images is now fixed on the femur_reflect_fix branch.
When you run the full use case with the --groom_images tag, then it gives the alignment error Alan mentioned above because the reflected segmentations are all zero. So anatomyPairsToSingles() in GroomUtils.py isn't working... @archanasri can you help us look at this?

jadie1 on 19 Feb 2021

@jadie1 @iyerkrithika21 could you try this:
img1.reflect(Axis.X).write(img_out) on line 312 of GroomUtils and
mesh.reflect(Axis.X, center).write(seg_out) on line 315 of GroomUtils

archanasri on 20 Feb 2021

@jadie1 @iyerkrithika21 could you try this:
img1.reflect(Axis.X).write(img_out) on line 312 of GroomUtils and
mesh.reflect(Axis.X, center).write(seg_out) on line 315 of GroomUtils

The reflected segmentations are still all zeros.
Saw the same error in the alignment.

iyerkrithika21 on 20 Feb 2021

Working when grooming without images as of PR #1030
Now fixing when grooming with images on branch reflect_fix

jadie1 on 22 Feb 2021

Fixed in PR #1040

jadie1 on 23 Feb 2021

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